Only fill the 40-man spots with players you need to protect from the Rule 5 draft or as you promote players to the majors. Once on the 40-man, you can't remove them without risking losing them. Open 40-man spots is a good thing, not a bad thing. You need to keep a 40-man spot open if you plan to take anyone in Rule 5, sign a free agent, or promote a player (not already on the 40) to the majors any time during the season.